Unlocking the Language of Cells

CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets.

Decipher single cells from the Tabula Sapiens dataset Explore the human transcriptome landscape in GEO Chat with colonic epithelium
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Spotlight paper @ ICLR 2024 MLGenX BioRxiv Code Generated datasets and models

Tutorial

(Click the annotated screenshot for a 2-minute video-tutorial)

Annotated screenshot of CellWhisperer application

Analyze your own data

To prepare your scRNA-seq data for use within CellWhisperer, follow these simple steps:

  1. Generate an h5ad file containing raw reads and a gene_name var column
  2. Run our single-command processing pipeline
  3. Start the CellWhisperer-integrated CELLxGENE Explorer
For details on these steps, refer to the "Analysis of new datasets with CellWhisperer" section in our README.

Citation

If you use CellWhisperer in your research, please cite the following preprint:

Moritz Schaefer*, Peter Peneder*, Daniel Malzl, Mihaela Peycheva, Jake Burton, Anna Hakobyan, Varun Sharma, Thomas Krausgruber, Jörg Menche, Eleni M. Tomazou, Christoph Bock (2024) Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats. bioRxiv, https://www.biorxiv.org/content/10.1101/2024.10.15.618501v1